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LOC126861567 CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:70636499-70637698 [ Homo sapiens (human) ]

Gene ID: 126861567, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126861567
Gene description
CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:70636499-70637698
Gene type
biological region
Feature type(s)
regulatory: enhancer, silencer
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic region was validated as an active enhancer by the STARR-seq (self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA) in HCT116 colorectal carcinoma cells, where it was defined as a group 2 enhancer that depends on the BRD2, BRD4, P300/CBP, MED14 and CDK7 cofactors, with strong dependence on CDK7. An accessible chromatin subregion was used in a lentiviral ReSE (repressive ability of silencer elements) screen that assays for cell survival based on transcriptional repression of an apoptosis-inducing fusion protein. That subregion was identified as a functional silencer in HepG2 liver carcinoma cells. This locus also includes two accessible chromatin subregions, one of which was validated as an enhancer and the other as a silencer based on their ability to activate or repress an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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See LOC126861567 in Genome Data Viewer
Location:
chromosome: 12
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (70242719..70243918)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (70222112..70223311)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene histone PARylation factor 1 pseudogene Neighboring gene MPRA-validated peak1797 silencer Neighboring gene MPRA-validated peak1798 silencer Neighboring gene long intergenic non-protein coding RNA 2821 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6658 Neighboring gene progenitor renewal associated non-coding RNA Neighboring gene MPRA-validated peak1799 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:70650862-70651362 Neighboring gene NANOG hESC enhancer GRCh37_chr12:70652346-70652879 Neighboring gene CCR4-NOT transcription complex subunit 2 Neighboring gene MPRA-validated peak1802 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4656 Neighboring gene MPRA-validated peak1805 silencer Neighboring gene potassium calcium-activated channel subfamily M regulatory beta subunit 4 Neighboring gene MPRA-validated peak1806 silencer Neighboring gene RNA, U4 small nuclear 65, pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Systematic identification of silencers in human cells. Pang B, et al. Nat Genet, 2020 Mar. PMID 32094911, Free PMC Article
  2. Differential cofactor dependencies define distinct types of human enhancers. Neumayr C, et al. Nature, 2022 Jun. PMID 35650434, Free PMC Article
  3. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, Free PMC Article

GeneRIFs: Gene References Into Functions

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 6657
  • ATAC-STARR-seq lymphoblastoid silent region 4655
  • ReSE screen-validated silencer GRCh37_chr12:70636632-70637171

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_086066.1 

    Range
    101..1300
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    70242719..70243918
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    70222112..70223311
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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